getFuncRvPosteriors {RIVER} | R Documentation

## Posterior probabilities of FR given G and E.

### Description

`getFuncRvPosteriors` computes posterior probabilities of functionality of regulatory variant (FR) given genomic features (G) and outlier status (E) with current estimate of beta (parameters between FR and G) and theta (parameters between FR and E).

### Usage

    getFuncRvPosteriors(Out, probFuncRvFeat, theta)

### Arguments

`Out` | Binary values of outlier status (E).
`probFuncRvFeat` | probabilities of FR given genomic features and estimated beta, P(FR | G, beta), from `getFuncRvFeat`.
`theta` | Current estimate of theta.

### Value

posterior probabilities of FR (P(FR | G, E, beta, theta)) and probable status of FR.

### Author(s)

Yungil Kim, ipw012@gmail.com

### Examples

    dataInput <- getData(filename=system.file("extdata", "simulation_RIVER.gz",
            package = "RIVER"), ZscoreThrd=1.5)
    Feat <- scale(t(Biobase::exprs(dataInput))) # genomic features (G)
    Out <- as.vector(as.numeric(unlist(dataInput$Outlier))-1) # outlier status (E)
    theta.init<-matrix(c(.99, .01, .3, .7), nrow=2)
    costs<-c(100, 10, 1, .1, .01, 1e-3, 1e-4)
    logisticAllCV <- glmnet::cv.glmnet(Feat, Out, lambda=costs, family="binomial",
            alpha=0, nfolds=10)
    probFuncRvFeat <- getFuncRvFeat(Feat, logisticAllCV$glmnet.fit,
            logisticAllCV$lambda.min)
    posteriors <- getFuncRvPosteriors(Out, probFuncRvFeat, theta=theta.init)

[Package RIVER version 1.4.0 Index]